Hi Tom

Thank you for getting back to me. It was very helpful.

Can the files you open be easily manipulated by selecting amino acids on the sequence or structure? Is there a way to superimpose and compare a protein bound with two different ligands?

Best

Reza

From: Tom Goddard <goddard@sonic.net>
Sent: January 27, 2025 3:39 PM
To: Reza Salavati, Prof. <reza.salavati@mcgill.ca>
Cc: chimerax-users@cgl.ucsf.edu; Artie Kushner <rtkushner@gmail.com>
Subject: Re: [chimerax-users] Chai discovery data

Hi Reza,

  Chai-1 outputs predicted aligned error (PAE) in .npy format.  You can open it in ChimeraX 1.9 by first opening the predicted structure pred.rank_0.cif using the File / Open dialog.  Then use menu Tools / Structure Prediction / AlphaFold Error Plot to open the PAE file pae.rank_0.npy.  This shows the PAE as a heat map as shown in the image below.  Use current ChimeraX version 1.9 not 1.8 since Chai-1 didn't exist when 1.8 was released and so the numpy PAE format was only added in 1.9.  For an explanation how to visualize that on the structure see this description

https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html

The scores.rank_0.json file contains summary confidence scores (per-chain pTM, between chain ipTM, ...) and clashes on a whole model or per-chain level.  ChimeraX doesn't have any tool to visualize those but you can show them in any  text editor, image below.

Tom

Chai-1 predicted structure and PAE plot shown in ChimeraX 1.9 (Nipah virus G protein with Zanamivir (pink) bound, low confidence).

Chai-1 scores.rank_0.json shown in a text editor

Files returned by Chai-1 server

On Jan 25, 2025, at 3:11 PM, Artie Kushner via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Reza, if you mean Chai the machine learning model/alphafold clone then you'd have to do a bit of work in connecting their output with Chimerax.

.npy files are generally the format in which python's `numpy` package saves multidimensional arrays to disk. I'm not sure what their json output is.

Your best bet is probably finding how the data in your files relates to chimerax' api and writing a script to connect the two.

On Sat, Jan 25, 2025 at 4:36 PM Reza Salavati, Prof. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I have downloaded the Chai discovery data in .npy and .json file formats.

How can I open these files in Chimera X?

Thank you

Reza

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